NIHVIVO-2049 fix so classes, classgroups, etc. don't get indexed

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoSDB.java

@@ -47,6 +47,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.IndividualSDB.IndividualNotFoundException;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode;
+import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 public class IndividualDaoSDB extends IndividualDaoJena {
 
@@ -333,8 +334,11 @@ public class IndividualDaoSDB extends IndividualDaoJena {
         final List<String> list = 
             new LinkedList<String>();
         
+        // get all labeled resources from any non-tbox and non-metadata graphs.
         String query = "SELECT DISTINCT ?ind WHERE { \n" +
                        "  GRAPH ?g { ?ind <" + RDFS.label.getURI() + "> ?label } \n" +
+                       "  FILTER (?g != <" + JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL + "> " +
+                       "          && !regex(str(?g),\"tbox\")) \n " +
                        "}";
               
 	    Query q = QueryFactory.create(query);

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupBase.java

@@ -110,7 +110,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
    
     // This model doesn't exist yet. It's a placeholder for the application 
     // ontology.
-    static final String JENA_APPLICATION_METADATA_MODEL = 
+    public static final String JENA_APPLICATION_METADATA_MODEL = 
         "http://vitro.mannlib.cornell.edu/default/vitro-kb-applicationMetadata";
    
     // This is Brian C's application.owl file. We may not have to be concerned 

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupSDB.java

@@ -36,6 +36,7 @@ import com.hp.hpl.jena.sdb.StoreDesc;
 import com.hp.hpl.jena.sdb.sql.SDBConnection;
 import com.hp.hpl.jena.sdb.store.DatabaseType;
 import com.hp.hpl.jena.sdb.store.LayoutType;
+import com.hp.hpl.jena.sdb.util.StoreUtils;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.util.iterator.ClosableIterator;
 import com.hp.hpl.jena.vocabulary.RDF;
@@ -317,6 +318,19 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
          
         } catch (MigrationRequiredError mre) {
         	throw new MigrationRequiredError(mre.getMessage());
+        } catch (SQLException sqle) {
+            
+            // SQL exceptions are fatal and should halt startup
+            AbortStartup.abortStartup(sce.getServletContext());
+            
+            log.error("Error using SQL database; startup aborted.", sqle);
+            
+            // print to catalina.out for good measure
+            System.out.println("Error using SQL database; startup aborted.");
+            sqle.printStackTrace();
+           
+            throw new Error(this.getClass().getName() + "failed");
+            
         } catch (Throwable t) {
             log.error("Throwable in " + this.getClass().getName(), t);
             // printing the error because Tomcat doesn't print context listener
@@ -616,6 +630,10 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
     	   	log.info("During initial SDB setup, created an application metadata model of size " 
     	   	        + applicationMetadataModel.size());
     	   	
+    	   	// remove application metadata from ABox model
+    	   	aboxAssertions.remove(applicationMetadataModel);
+    	   	aboxInferences.remove(applicationMetadataModel);
+                    
             // Make sure the reasoner takes into account the newly-set-up data.
             SimpleReasonerSetup.setRecomputeRequired(ctx);
         
@@ -631,12 +649,13 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
      * @param store
      * @return
      */
-    private boolean isSetUp(Store store) {
+    private boolean isSetUp(Store store) throws SQLException {
-        try {
+        return StoreUtils.isFormatted(store);
-            return (SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL)).size() > 0;    
+//        try {
-        } catch (Exception e) { 
+//            return (SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL)).size() > 0;    
-            return false;
+//        } catch (Exception e) { 
-        }
+//            return false;
+//        }
     }
     
     private static final String STOREDESC_ATTR = "storeDesc";